Posts by liorglic

... Thanks I understand now. I decided to try a wrapper tool called DRAP (https://peerj.com/articles/2988/) which has a module called runMeta. It uses CD-HIT-EST to collapse transcripts and the assembler TGICL to elongate transcripts. I'll see how this works for me. ...

... Thanks @mks002. I am familiar with CD-HIT, and have seen it mentioned in this context before, but I still don't understand how it can solve my problem. CD-HIT clusters transcripts based on a similarity threshold. How can such output be used to actually merge transcripts together? Can you explain in ...

... Hi everyone. Need your advice on an issue I'm having.
So, I have used Trinity in order to create transcriptome assemblies from ~30 data sets of RNA-Seq, downloaded from SRA. All data sets come from the same species (tomato), but from different variants, conditions and tissues. My aim is to produce ...

... Hello,
I've ran [TopHat][1] and aligned paired end (PE) reads to a reference genome.
TopHat outputs two bam files: accepted_hits.bam and unmapped.bam.
I'd like to extract from unmapped.bam only those reads where only one side of the pair (R1 or R2) was not mapped, i.e. exclude records where bo ...

... Hi
I am collecting RNA-Seq data from NCBI SRA for a specific organism, in order to create a de-novo transcriptome assembly.
For each data set archived in SRA, the "Library Selection" field is given, usually indicating either "cDNA", "EST" or "RANDOM". According to [this page][1], the definitions ...

... Yes, if I look at other varieties/cultivars other than the one used to produce the reference (Heinz). This had not yet been done in tomato, but in other organisms (e.g rice and maize) non-reference cultivars showed a substantial amount of novel genes not found in the reference. ...

... Thank you. This is very helpful.
As I said, I'm not planning on producing new RNA-seq data right now, but rather use data available from various DBs. So for example I found a data set comprised of ~2.8Gb sequencing data, with reads of length 61. Would you consider assembling this or would you say ...

... Hello,
I'm rather new to RNA-seq analysis and more familiar with DNA sequencing.
I'd like to perform de-novo assembly of transcripts from publicly-available (i.e published) RNA-seq data in tomato and its wild relative. the reasons I need to do that are:
a. I want to discover novel genes not pr ...

... Thanks, I wasn't familiar with this software. However, since I'm also interested in detecting new genes not present in the reference annotation, I'd like to use the transcriptomic data on top of that, and this is where most of the noise comes from. ...